Table 1.
GyDB 2.0 new features: topics and contents
| Systems | Families | Lineages | Elements | Protein domains | Accessory proteins | LTRs |
|---|---|---|---|---|---|---|
| LTR retroelements | Ty3/Gypsy | 34 | 96 | 8 | 1 | Yes |
| LTR retroelements | Ty1/Copia | 19 | 69 | 8 | – | Yes |
| LTR retroelements | Retroviridae | 8 | 50 | 8 | 41 | Yes |
| LTR retroelements | Bel/Pao | 5 | 23 | 7 | – | Yes |
| LTR retroelementsa | Caulimoviridae | 6 | 30 | 10 | 27 | No |
| Related families | Clan AA | 35 | 323 | 1 | – | No |
| Related families | Chromodomains | 2 | 123 | 1 | – | No |
| Topics | Sections | Availability |
|---|---|---|
| Systematics | 9 | Side menu |
| Domains | 14 | Side menu |
| Database | 8 | Side menu |
| Servers | 3 | Top menu: BLAST, HMM, Literature |
| Wiki tools and utilities | 3 | Top menu |
| Databases | Items | Sections | |
|---|---|---|---|
| Genomes (full-length genomes) | 271 | sequences | BLAST search and RefSeq DBs |
| LTRs (nucleotide sequences) | 413 | sequences | BLAST search and RefSeq DBs |
| Cores (protein cores sequences) | 1895 | sequences | BLAST search and RefSeq DBs |
| HMMs | 314 | HMM profiles | HMM search and GyDB collection |
| Multiple alignments | 131 | alignments | GyDB collection |
| Consensus sequences | 314 | MRC sequences | GyDB collection |
| Phylogenetic trees | 70 | trees | Phylogenies |
| Clan AA ancestral reconstruction | 70 | alignments | CAARD database |
| Literature | 100797 | references | Literature server |
aWe included caulimoviruses in the second release in view of their relationship with LTR retroelements based on the common gag/coat and pol region.